Stuart Levine

Enhancer Reprogramming in Melanoma Immune Checkpoint Therapy Resistance

Jan 2022

preprint

A single-cell liver atlas of Plasmodium vivax infection.

Cell host & microbe

Jan 2022

journal-article

NExtSEEK: Extending SEEK for Active Management of Interoperable Metadata.

Journal of biomolecular techniques : JBT

Jan 2022

journal-article

Developmental Deconvolution for Classification of Cancer Origin.

Cancer discovery

Jan 2022

journal-article

Myeloid cell subsets that express latency-associated peptide promote cancer growth by modulating T cells.

iScience

Jan 2021

journal-article

Developmental Deconvolution for Classification of Cancer Origin

Jan 2021

preprint

Gene signatures and host-parasite interactions revealed by dual single-cell profiling of Plasmodium vivax liver infection

Jan 2021

preprint

Quantitative mapping of the cellular small RNA landscape with AQRNA-seq.

Nature biotechnology

Jan 2021

journal-article

Human physiomimetic model integrating microphysiological systems of the gut, liver, and brain for studies of neurodegenerative diseases.

Science advances

Jan 2021

journal-article

Benchmarking cDNA sequencing on PromethION

Journal of biomolecular techniques : JBT

Jan 2020

journal-article

Bioinformatics Core Survey Highlights the Challenges Facing Data Analysis Facilities.

Journal of biomolecular techniques : JBT

Jan 2020

journal-article

Multisite Evaluation of Next-Generation Methods for Small RNA Quantification.

Journal of biomolecular techniques : JBT

Jan 2020

journal-article

SPRI Beads-based Size Selection in the Range of 2-10kb.

Journal of biomolecular techniques : JBT

Jan 2020

journal-article

High-throughput Minitaturized RNA-Seq Library Preparation.

Journal of biomolecular techniques : JBT

Jan 2020

journal-article

Cross-Site Evaluation of Commercial Sanger Sequencing Chemistries.

Journal of biomolecular techniques : JBT

Jan 2020

journal-article

A set of miniaturized high-throughput library protocols for RNA sequencing

Journal of biomolecular techniques : JBT

Jan 2020

journal-article

HONEY I SHRUNK THE KITS: Practical Adventures in Reducing Assay Volumes

Journal of biomolecular techniques : JBT

Jan 2020

journal-article

Ketone Body Signaling Mediates Intestinal Stem Cell Homeostasis and Adaptation to Diet.

Cell

Jan 2019

journal-article

Stabilization of the Max Homodimer with a Small Molecule Attenuates Myc-Driven Transcription.

Cell chemical biology

Jan 2019

journal-article

Encapsulated miR-200c and Nkx2.1 in a nuclear/mitochondria transcriptional regulatory network of non-metastatic and metastatic lung cancer cells.

BMC cancer

Jan 2019

journal-article

Global transcriptional regulation of innate immunity by ATF-7 in C. elegans.

PLoS genetics

Jan 2019

journal-article

Cross Site Evaluation of Sanger Sequencing Dye Chemistries

Journal of biomolecular techniques : JBT

Jan 2019

journal-article

GBIRG Bioinformatics Core Survey Highlights the Challenges Facing Data Analysis Facilities

Journal of biomolecular techniques : JBT

Jan 2019

journal-article

Miniaturization of Illumina Library Preparation for High Throughput, Plate-Based Next Generation Sequencing Studies

Journal of biomolecular techniques : JBT

Jan 2019

journal-article

Sequencing-based quantitative mapping of the cellular small RNA landscape

Jan 2019

preprint

Single-cell transcriptomic profiling of the aging mouse brain.

Nature neuroscience

Jan 2019

journal-article

H3K27me3-mediated silencing of structural genes is required for zebrafish heart regeneration.

Development (Cambridge, England)

Jan 2019

journal-article

HRI coordinates translation necessary for protein homeostasis and mitochondrial function in erythropoiesis.

eLife

Jan 2019

journal-article

Global transcriptional regulation of innate immunity in C. elegans

Jan 2018

other

Iron and Heme Coordinate Erythropoiesis through HRI-Mediated Regulation of Protein Translation and Gene Expression

Jan 2018

other

Single-cell transcriptomics of the aged mouse brain reveals convergent, divergent and unique aging signatures

Jan 2018

preprint

In Vitro Culture, Drug Sensitivity, and Transcriptome of Plasmodium Vivax Hypnozoites.

Cell host & microbe

Jan 2018

journal-article

Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction.

BMC genomics

Jan 2018

journal-article

Cross-Site Comparison of Ribosomal Depletion Kits for Illumina RNAseq Library Construction

Jan 2017

other

Host proteostasis modulates influenza evolution.

eLife

Jan 2017

journal-article

The Hox proteins Ubx and AbdA collaborate with the transcription pausing factor M1BP to regulate gene transcription.

The EMBO journal

Jan 2017

journal-article

Mutational spectra of aflatoxin B1 in vivo establish biomarkers of exposure for human hepatocellular carcinoma.

Proceedings of the National Academy of Sciences of the United States of America

Jan 2017

journal-article

Monitoring Error Rates In Illumina Sequencing.

Journal of biomolecular techniques : JBT

Jan 2016

journal-article

RNA polymerase II promoter-proximal pausing in mammalian long non-coding genes.

Genomics

Jan 2016

journal-article

Next-generation sequencing reveals the biological significance of the N(2),3-ethenoguanine lesion in vivo.

Nucleic acids research

Jan 2015

journal-article

Transportable, Chemical Genetic Methodology for the Small Molecule-Mediated Inhibition of Heat Shock Factor 1.

ACS chemical biology

Jan 2015

journal-article

Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences.

Nature communications

Jan 2014

journal-article

TRIM28 regulates RNA polymerase II promoter-proximal pausing and pause release.

Nature structural & molecular biology

Jan 2014

journal-article

Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis.

Environmental Health Perspectives

Jan 2014

journal-article

Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number.

Nucleic acids research

Jan 2014

journal-article

Polycomb Repressive Complex 2 regulates lineage fidelity during embryonic stem cell differentiation.

PloS one

Jan 2014

journal-article

H2A.Z acidic patch couples chromatin dynamics to regulation of gene expression programs during ESC differentiation.

PLoS genetics

Jan 2013

journal-article

Which RNA-Seq Processing Algorithm Should I Pick? A Comparison of RNA-Seq Pipelines Based on Experimental Design, Sample Properties and Sequencing Technology.

Journal of biomolecular techniques : JBT

Jan 2013

journal-article

Gut microbiome perturbations induced by bacterial infection affect arsenic biotransformation.

Chemical research in toxicology

Jan 2013

journal-article

Lane-by-lane sequencing using Illumina's Genome Analyzer II.

BioTechniques

Jan 2013

journal-article

Admixture and recombination among Toxoplasma gondii lineages explain global genome diversity.

Proceedings of the National Academy of Sciences of the United States of America

Jan 2012

journal-article

Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage.

Cell

Jan 2012

journal-article

Comparison of SYBR Enzymes and Standards in Illumina Library Quantification.

Journal of biomolecular techniques : JBT

Jan 2011

journal-article

miR-132, an experience-dependent microRNA, is essential for visual cortex plasticity.

Nature neuroscience

Jan 2011

journal-article

Mediator and cohesin connect gene expression and chromatin architecture.

Nature

Jan 2010

journal-article

Ronin/Hcf-1 binds to a hyperconserved enhancer element and regulates genes involved in the growth of embryonic stem cells.

Genes & development

Jan 2010

journal-article

Effects of age on meiosis in budding yeast.

Developmental cell

Jan 2009

journal-article

H2AZ is enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment.

Cell

Jan 2008

journal-article

Divergent transcription from active promoters.

Science (New York, N.Y.)

Jan 2008

journal-article

Aberrant chromatin at genes encoding stem cell regulators in human mixed-lineage leukemia.

Genes & development

Jan 2008

journal-article

Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells.

Cell

Jan 2008

journal-article

A chromatin landmark and transcription initiation at most promoters in human cells.

Cell

Jan 2007

journal-article

Foxp3 occupancy and regulation of key target genes during T-cell stimulation.

Nature

Jan 2007

journal-article

Control of developmental regulators by Polycomb in human embryonic stem cells.

Cell

Jan 2006

journal-article

Polycomb complexes repress developmental regulators in murine embryonic stem cells.

Nature

Jan 2006

journal-article

Genome-wide map of nucleosome acetylation and methylation in yeast.

Cell

Jan 2005

journal-article

The core centromere and Sgo1 establish a 50-kb cohesin-protected domain around centromeres during meiosis I.

Genes & development

Jan 2005

journal-article

Core transcriptional regulatory circuitry in human embryonic stem cells.

Cell

Jan 2005

journal-article

Division of labor in polycomb group repression.

Trends in biochemical sciences

Jan 2004

journal-article

Menin associates with a trithorax family histone methyltransferase complex and with the hoxc8 locus.

Molecular cell

Jan 2004

journal-article

The core of the polycomb repressive complex is compositionally and functionally conserved in flies and humans.

Molecular and cellular biology

Jan 2002

journal-article

Stuart Levine

Work

Massachusetts Institute of Technology

Whitehead Institute for Biomedical Research

Education

Harvard University

Massachusetts Institute of Technology

Publications

Enhancer Reprogramming in Melanoma Immune Checkpoint Therapy Resistance

A single-cell liver atlas of Plasmodium vivax infection.

NExtSEEK: Extending SEEK for Active Management of Interoperable Metadata.

Developmental Deconvolution for Classification of Cancer Origin.

Myeloid cell subsets that express latency-associated peptide promote cancer growth by modulating T cells.

Developmental Deconvolution for Classification of Cancer Origin

Gene signatures and host-parasite interactions revealed by dual single-cell profiling of Plasmodium vivax liver infection

Quantitative mapping of the cellular small RNA landscape with AQRNA-seq.

Human physiomimetic model integrating microphysiological systems of the gut, liver, and brain for studies of neurodegenerative diseases.

Benchmarking cDNA sequencing on PromethION

Bioinformatics Core Survey Highlights the Challenges Facing Data Analysis Facilities.

Multisite Evaluation of Next-Generation Methods for Small RNA Quantification.

SPRI Beads-based Size Selection in the Range of 2-10kb.

High-throughput Minitaturized RNA-Seq Library Preparation.

Cross-Site Evaluation of Commercial Sanger Sequencing Chemistries.

A set of miniaturized high-throughput library protocols for RNA sequencing

HONEY I SHRUNK THE KITS: Practical Adventures in Reducing Assay Volumes

Ketone Body Signaling Mediates Intestinal Stem Cell Homeostasis and Adaptation to Diet.

Stabilization of the Max Homodimer with a Small Molecule Attenuates Myc-Driven Transcription.

Encapsulated miR-200c and Nkx2.1 in a nuclear/mitochondria transcriptional regulatory network of non-metastatic and metastatic lung cancer cells.

Global transcriptional regulation of innate immunity by ATF-7 in C. elegans.

Cross Site Evaluation of Sanger Sequencing Dye Chemistries

GBIRG Bioinformatics Core Survey Highlights the Challenges Facing Data Analysis Facilities

Miniaturization of Illumina Library Preparation for High Throughput, Plate-Based Next Generation Sequencing Studies

Sequencing-based quantitative mapping of the cellular small RNA landscape

Single-cell transcriptomic profiling of the aging mouse brain.

H3K27me3-mediated silencing of structural genes is required for zebrafish heart regeneration.

HRI coordinates translation necessary for protein homeostasis and mitochondrial function in erythropoiesis.

Global transcriptional regulation of innate immunity in C. elegans

Iron and Heme Coordinate Erythropoiesis through HRI-Mediated Regulation of Protein Translation and Gene Expression

Single-cell transcriptomics of the aged mouse brain reveals convergent, divergent and unique aging signatures

In Vitro Culture, Drug Sensitivity, and Transcriptome of Plasmodium Vivax Hypnozoites.

Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction.

Cross-Site Comparison of Ribosomal Depletion Kits for Illumina RNAseq Library Construction

Host proteostasis modulates influenza evolution.

The Hox proteins Ubx and AbdA collaborate with the transcription pausing factor M1BP to regulate gene transcription.

Mutational spectra of aflatoxin B1 in vivo establish biomarkers of exposure for human hepatocellular carcinoma.

Monitoring Error Rates In Illumina Sequencing.

RNA polymerase II promoter-proximal pausing in mammalian long non-coding genes.

Next-generation sequencing reveals the biological significance of the N(2),3-ethenoguanine lesion in vivo.

Transportable, Chemical Genetic Methodology for the Small Molecule-Mediated Inhibition of Heat Shock Factor 1.

Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences.

TRIM28 regulates RNA polymerase II promoter-proximal pausing and pause release.

Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis.

Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number.

Polycomb Repressive Complex 2 regulates lineage fidelity during embryonic stem cell differentiation.

H2A.Z acidic patch couples chromatin dynamics to regulation of gene expression programs during ESC differentiation.

Which RNA-Seq Processing Algorithm Should I Pick? A Comparison of RNA-Seq Pipelines Based on Experimental Design, Sample Properties and Sequencing Technology.

Gut microbiome perturbations induced by bacterial infection affect arsenic biotransformation.

Lane-by-lane sequencing using Illumina's Genome Analyzer II.

Admixture and recombination among Toxoplasma gondii lineages explain global genome diversity.

Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage.

Comparison of SYBR Enzymes and Standards in Illumina Library Quantification.

miR-132, an experience-dependent microRNA, is essential for visual cortex plasticity.

Mediator and cohesin connect gene expression and chromatin architecture.

Ronin/Hcf-1 binds to a hyperconserved enhancer element and regulates genes involved in the growth of embryonic stem cells.

Effects of age on meiosis in budding yeast.

H2AZ is enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment.

Divergent transcription from active promoters.

Aberrant chromatin at genes encoding stem cell regulators in human mixed-lineage leukemia.

Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells.

A chromatin landmark and transcription initiation at most promoters in human cells.

Foxp3 occupancy and regulation of key target genes during T-cell stimulation.

Control of developmental regulators by Polycomb in human embryonic stem cells.

Polycomb complexes repress developmental regulators in murine embryonic stem cells.

Genome-wide map of nucleosome acetylation and methylation in yeast.

The core centromere and Sgo1 establish a 50-kb cohesin-protected domain around centromeres during meiosis I.

Core transcriptional regulatory circuitry in human embryonic stem cells.

Division of labor in polycomb group repression.

Menin associates with a trithorax family histone methyltransferase complex and with the hoxc8 locus.

The core of the polycomb repressive complex is compositionally and functionally conserved in flies and humans.